Barley: Emergence as a New Research Material of Crop Science

The completion of genome sequencing, advances in a wide range of analytic technologies, greater research platforms and the emergence of bioinformatics procedures, as well as the development of related resources, have contributed to improvements in the quality of research not only in model species but also in crop plants and livestock. Sustainable agricultural production is an urgent issue in the context of global climate change and food security (Brown and Funk 2008, Turner et al. 2009). In order to address this issue, the integration of a broad spectrum of analytical tools and resources and an understanding of genetic mechanisms for agriculturally important traits is needed (Yamamoto et al. 2009, Mochida and Shinozaki 2010). Several essential features of barley (Hordeum vulgare L.) contribute to the broad utilization of this crop in genetic studies. These features include (i) the crop's diploid nature with a high degree of inbreeding; (ii) the low chromosome number (2n = 14) with large size; (iii) the ease of cross-breeding; and (iv) the ease of cultivation in a wide range of climatic conditions. Cultivated barley, which ranks fourth among cereals with respect to worldwide production, is also well known as an extensively studied plant species in the field of genetics. Regarding its geographic adaptability, barley is particularly noted for its tolerance to cold, drought, alkalinity and salinity. In recent years, to address its huge genome size (∼5,000 Mb), research resources essential for barley genomic studies have been developed, including a large number of expressed sequence tags (ESTs). These have been widely used for barley genome analyses such as DNA marker generation and the construction of microarrays. Recent innovations in sequencing technology, which allow for working on a massive scale by genotyping thousands of single nucleotide polymorphisms (SNPs) on a genome-wide scale, have enabled us to dissect many genetically and biologically agronomically important complex traits. Advanced mapping populations, including chromosome segment substitution lines (CSSLs), have worked as the engines of genetic dissection of quantitative trait loci (QTLs) (Fukuoka et al. 2010). Resources for barley functional genomics have improved over the last decade, and several high-density genetic maps utilizing various types of molecular markers have been constructed (Close et al. 2009, Schulte et al. 2009). Several CSSLs have also been developed, and these are being used for various QTL discovery and related analyses in barley (e.g. Hori et al. 2005). Furthermore, >370,000 barley germplasms are preserved as ex situ collections in representative genebanks, including Okayama University (http://www.shigen.nig.ac.jp/barley/), and worldwide. In this special issue on barley in Plant and Cell Physiology, we discuss the historic advantages of barley as a genetic research material, as well as crop improvements, and briefly outline recent achievements in the establishment of genomic infrastructure that have enabled us to examine the characteristic traits of barley and/or to compare findings with other plant species such as Arabidopsis, rice, maize and soybean. Sato et al. (pp. 728–737) provided new barley research resources in the form of a doubled haploid population derived from the cross between the malting variety ‘Haruna Nijo’ and the Japanese landrace ‘Akashinriki,’ as well as 35 CSSL introgressions from ‘Akashinriki’ on a ‘Haruna Nijo’ background. Several genes controlling barley flower and inflorescence morphology have been isolated by means of map-based cloning technology, including the genes encoding the six-rowed spike (Komatsuda et al. 2007) and naked caryopsis (Taketa et al. 2008). These morphological characteristics and the non-brittleness (grain shattering) of barley are well-known characteristic traits of domesticated barley, and a model of the barley domestication process has been developed based on archeological evidence of these characteristics (Zohary and Hopf 2000). Sakuma et al. (pp. 738–749) provides an overview of the disarticulation systems and inflorescence characteristics, along with the genes underlying these traits, occurring in the Triticeae tribe. In spite of its large genome, barley is recognized as a good genomic model of the Triticeae tribe, which includes cultivated wheat (einkorn, durum and bread wheats), rye and their respective wild relatives (Schulte et al. 2009). The evolution of the polyploid wheats is distinctive in that domestication, natural hybridization and allopolyploid speciation have significant impacts on their diversification. In this special issue, Matsuoka (pp. 750–764) outlines the phylogenetic relationship between cultivated wheats and their wild relatives and provides an overview of the recent progress and remaining questions in our understanding of the genetic and ecological factors that have favored their evolution. Among graminaceous plants, barley is one of the species that is most tolerant to iron deficiency. The HvYS1 gene has been identified as encoding an iron–phytosiderophore transporter that secretes phytosiderophores in response to iron deficiency (Murata et al. 2006). In this special issue on barley, Zheng et al. (pp. 765–774) newly characterized one of the unidentified members of the yellow stripe-like (YSL) family transporters, HvYSL5. The HvYSL5 gene was found to be expressed in the roots, and this expression was greatly induced by iron deficiency, but not by a deficiency of other metals. This research will provide novel opportunities to uncover the transient storage mechanisms of iron or phytosiderophores in barley. Prolonged exposure to low winter temperatures before flowering, i.e. vernalization, is one of the key cues to determining the ideal flowering time of many plant species such as Arabidopsis, wheat and barley. Genetic variations in vernalization requirements are believed to be one of the main evolutionary driving forces for the broad adaptability of cereals. In order to address the extent of natural variation in vernalization requirements and its relationship to the plant's geographic distribution, Saisho et al. (pp. 775–784) performed a large-scale investigation of vernalization requirements using barley germplasm and depicted the geographic distribution pattern of differing vernalization requirements. Based on the developed infrastructure for barley genomic resources, the Affymetrix GeneChip was designed using tentative consensus transcribed sequences that were obtained mainly from clustered ESTs as a representative transcriptome platform (Close et al. 2004), and several large-scale gene expression analyses of barley have been conducted (e.g. Druka et al. 2006). In this special issue, Mochida et al. (pp. 785–803) describe the construction of a co-expression network using >1,000 sets of Affymetrix GeneChip data derived from 45 publicly available experimental series. This approach may provide us with new possibilities for identifying transcriptional regulatory networks, which may be specific or well-diverged genes in Triticeae species. In Okayama University, which is recognized as the Asian center of barley germplasm of the world, efforts to generate induced mutants are ongoing (e.g. Konishi 1976). Further, several hundred barley genetic stock (BGS) accessions, including induced mutants, linkage testers and near isogenic lines (NILs), are also preserved and have been widely used as research materials for the morphological and physiological characterization of barley (Figure 1). Phenotypes of barley genetic stocks and natural variations. (A) Two-rowed (left 2) and six-rowed spikes (vrs1; BGS6/GSHO196, right 6) with variations in the awn length of the central and lateral spikelets. (B) Naked (nud; BGS7/GSHO115, left) and covered (right) caryopses. (C) Brachytic 1 (brh1; BGS1/GSHO25) in ‘Akashinriki’, harboring uzu (see F). (D) Xantha seedling 1 (Xnt1; BGS25/GSHO1606). (E) Pigmented variations of the kernel (left) and lemma (centre and right). (F) Uzu or semi-brachytic dwarf (uzu; BGS102/GSHO1300, right) and normal NIL (left). (G) White streak (wst6; BGS129/GSHO2500) seedling. (H) Dense spike (dsp9; BGS258/GSHO1774, left) and normal type (right). (I) Necrotic leaf spot (nec5; BGS139/OUM372, right) and normal leaf blade (left). (J) Short crooked awn (sca; BGS128/GSHO2439). (K) Curly dwarf (cud1; BGS324/GSHO1711) in ‘Akashinriki’. (L) Severe (left) and no (right) signs of barley yellow mosaic virus in the field. (M) Sensitive (left) and tolerant (right) variations of flooding tolerance. (N) Resistance, moderate resistance and susceptibility (left to right) to powdery mildew. In 1996, by the extensive efforts of Francowiak, Lundqvist and Konishi, as well as a broad range of barley researchers, 589 lines of BGS were collected and listed with comprehensive descriptions of several genetic characteristics, including phenotypic characteristics, inheritance, origin of mutants and related references. The list was published as a special issue in the Barley Genetics Newsletter (Lundqvist et al. 1997; http://wheat.pw.usda.gov/ggpages/bgn/26/bgn26tc.html). The extension of BGS lines and their characterization is continuing and has improved substantially, with the stocks reaching 661 lines in 2008 (http://wheat.pw.usda.gov/ggpages/bgn/38/BarleyGeneticStocksBGN38.htm). The seed stock associated with each BGS number is held as a GSHO stock number and is freely available through the USDA-ARS National Small Grains Germplasm Research Facility, Aberdeen, ID, USA (http://www.ars-grin.gov/npgs/searchgrin.html). In addition, an extensive backcrossing program was initiated in the mid-1980s to introgress mutated loci from the worldwide collection of morphological and developmental mutants into a common genetic background, the cultivar ‘Bowman’. The final collection of 881 lines varied in genetic complexity from F1 inbred lines to BC10 inbred lines. Recently, Druka et al. (2011) genotyped the 881 NILs up to 3,072 SNPs and, by comparison with their recurrent parent, defined the genetic location of 426 mutant alleles to chromosomal segments. Adopting a combined approach for barley genetics using the improved genetic resources developed by the efforts of pioneers with great foresight and the genomic infrastructure that is rapidly developing using high-throughput advanced technology promises to accelerate our understanding of the molecular functions of barely genes, responsible not only for qualitative morphological and physiological traits, but also for quantitative and complex agronomic traits. barley genetic stock chromosome segment substitution line expressed sequence tag near isogenic line quantitative trait locus single nucleotide polymorphism yellow stripe-like